rs200116

Positions:

• chr5-8650219-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.134 in 152,154 control chromosomes in the GnomAD database, including 1,634 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1634 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20381 AN: 152036 Hom.: 1634 Cov.: 32

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.148

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.134 AC: 20379 AN: 152154 Hom.: 1634 Cov.: 32 AF XY: 0.138 AC XY: 10236 AN XY: 74378

Gnomad4 AFR AF: 0.0664

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.149

Alfa AF: 0.145 Hom.: 1679

Bravo AF: 0.126

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs200116; hg19: chr5-8650331;